Man pages for HenrikBengtsson/affxparser
Affymetrix File Parsing SDK

1._Dictionary	1. Dictionary
2._Cell_coordinates_and_cell_indices	2. Cell coordinates and cell indices
9._Advanced_-_Cell-index_maps_for_reading_and_writing	9. Advanced - Cell-index maps for reading and writing
affxparser-package	Package affxparser
applyCdfGroupFields	Applies a function to a list of fields of each group in a CDF...
applyCdfGroups	Applies a function over the groups in a CDF structure
arrangeCelFilesByChipType	Moves CEL files to subdirectories with names corresponding to...
cdfAddBaseMmCounts	Adds the number of allele A and allele B mismatching...
cdfAddPlasqTypes	Adds the PLASQ types for the probes in a CDF structure
cdfAddProbeOffsets	Adds probe offsets to the groups in a CDF structure
cdfGetFields	Gets a subset of groups fields in a CDF structure
cdfGetGroups	Gets a subset of groups in a CDF structure
cdfGtypeCelToPQ	Function to imitate Affymetrix' gtype_cel_to_pq software
cdfHeaderToCelHeader	Creates a valid CEL header from a CDF header
cdfMergeAlleles	Function to join CDF allele A and allele B groups strand by...
cdfMergeStrands	Function to join CDF groups with the same names
cdfMergeToQuartets	Function to re-arrange CDF groups values in quartets
cdfOrderBy	Orders the fields according to the value of another field in...
cdfOrderColumnsBy	Orders the columns of fields according to the values in a...
cdfSetDimension	Sets the dimension of an object
compareCdfs	Compares the contents of two CDF files
compareCels	Compares the contents of two CEL files
convertCdf	Converts a CDF into the same CDF but with another format
convertCel	Converts a CEL into the same CEL but with another format
copyCel	Copies a CEL file
createCel	Creates an empty CEL file
findCdf	Search for CDF files in multiple directories
findFiles	Finds one or several files in multiple directories
invertMap	Inverts a read or a write map
isCelFile	Checks if a file is a CEL file or not
parseDatHeaderString	Parses a DAT header string
readBpmap	Parses a Bpmap file
readCcg	Reads an Affymetrix Command Console Generic (CCG) Data file
readCcgHeader	Reads an the header of an Affymetrix Command Console Generic...
readCdf	Parsing a CDF file using Affymetrix Fusion SDK
readCdfCellIndices	Reads (one-based) cell indices of units (probesets) in an...
readCdfDataFrame	Reads units (probesets) from an Affymetrix CDF file
readCdfGroupNames	Reads group names for a set of units (probesets) in an...
readCdfHeader	Reads the header associated with an Affymetrix CDF file
readCdfIsPm	Checks if cells in a CDF file are perfect-match probes or not
readCdfNbrOfCellsPerUnitGroup	Gets the number of cells (probes) that each group of each...
readCdfQc	Reads the QC units of CDF file
readCdfUnitNames	Reads unit (probeset) names from an Affymetrix CDF file
readCdfUnits	Reads units (probesets) from an Affymetrix CDF file
readCdfUnitsWriteMap	Generates an Affymetrix cell-index write map from a CDF file
readCel	Reads an Affymetrix CEL file
readCelHeader	Parsing the header of an Affymetrix CEL file
readCelIntensities	Reads the intensities contained in several Affymetrix CEL...
readCelRectangle	Reads a spatial subset of probe-level data from Affymetrix...
readCelUnits	Reads probe-level data ordered as units (probesets) from one...
readChp	A function to read Affymetrix CHP files
readClf	Parsing a CLF file using Affymetrix Fusion SDK
readClfEnv	Parsing a CLF file using Affymetrix Fusion SDK
readClfHeader	Read the header of a CLF file.
readPgf	Parsing a PGF file using Affymetrix Fusion SDK
readPgfEnv	Parsing a PGF file using Affymetrix Fusion SDK
readPgfHeader	Read the header of a PGF file into a list.
updateCel	Updates a CEL file
updateCelUnits	Updates a CEL file unit by unit
writeCdf	Creates a binary CDF file
writeCdfHeader	Writes a CDF header
writeCdfQcUnits	Writes CDF QC units
writeCdfUnits	Writes CDF units
writeCelHeader	Writes a CEL header to a connection
writeTpmap	Writes BPMAP and TPMAP files.